Not in comic books, though; rather, in popular culture in general.
On my short list, I'd include the modern horror trio - Freddy Krueger, Jason Voorhees and Michael Myers - the modern sci-fi trio - the Alien, the Predator and the Terminator - and one archvillain from each of those two categories - Hannibal Lecter and Darth Vader.
Yes, I'm being inspired by an underused plot point from The Last Action Hero, but I think I can apply it to the Parodyverse in an interesting way, and I already know how to apply it to CrazySugarFreakBoy! in an interesting way.
So, if your characters were to face off against famous non-superhero villains, which ones would you want to write about?

I wouldn't call most of these villains "iconic", but they're probably my top ten outside of the comic books. In no particular order:

Hannibal Lecter
Mr Potter
Leonard Smalls
Jafar
Hans Gruber
Duchess (The cat from "Babe")
Clubber Lang
Noah Cross
Scar
Nurse Ratched

You two have already hit many of the big ones. Mine aren't all household names, by any means (although you can easily pick out which ones are, obviously.)

Films:
Agent Smith
Keyser Soze
Clarence Boddicker
Angel Eyes

Monsters:
Godzilla
Audrey II
The Thing

Literature:
Grendel
Captain Nemo
Prof. Moriarty
The Grinch
Shere Khan
Smaug

Television:
Angelus
Xena (she started as a villain, for those who don't remember)
Eric Cartman
Dr. Zachary Smith
Cancer Man aka Cigarette Smoking Man
Montgomery Burns
Endora

Video Games:
Donkey Kong
Carmen Sandiego
Scorpion and/or Sub-Zero
Psycho Mantis
GLaDOS

Classic!
The only ones I'd add to those already mentioned in this thread are the Daleks, Norman Bates, Dracula (the novel version please) and Annie Wilkes.
If we can choose historical figures I'd add some more.
 
Al B.

Ernst Blofeld for a bit of fun.